Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.001397/0.001397, allocations: 99.64 kB / 18.94 MB, free: 2.551 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.001634/0.001634, allocations: 212.3 kB / 22.24 MB, free: 4.855 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 1.425/1.425, allocations: 230.6 MB / 256 MB, free: 7.809 MB / 206.1 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.142/0.142, allocations: 23.89 MB / 336.3 MB, free: 10.95 MB / 270.1 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
"Notification: Chemical requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.001991/0.001991, allocations: 66.72 kB / 471.6 MB, free: 7 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3415/0.3435, allocations: 59.85 MB / 0.519 GB, free: 9.773 MB / 382.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66:writable] Notification: The diagnostics message for the missing inner is: 
Your model is using an outer \"system\" component but
an inner \"system\" component is not defined.
For simulation drag Modelica.Fluid.System into your model
to specify system properties.
Notification: Performance of NFInst.instantiate(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis): time 0.07961/0.4231, allocations: 26.21 MB / 0.5446 GB, free: 13.44 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02154/0.4447, allocations: 14.72 MB / 0.559 GB, free: 60 kB / 398.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001005/0.4457, allocations: 15.88 kB / 0.559 GB, free: 44 kB / 398.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0012/0.4469, allocations: 312.4 kB / 0.5593 GB, free: 15.81 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004833/0.4517, allocations: 1.468 MB / 0.5607 GB, free: 14.57 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005956/0.4577, allocations: 2.026 MB / 0.5627 GB, free: 12.9 MB / 414.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002556/0.4602, allocations: 1.543 MB / 0.5642 GB, free: 11.51 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001273/0.4615, allocations: 0.6932 MB / 0.5649 GB, free: 10.89 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.00124/0.4627, allocations: 0.7871 MB / 0.5657 GB, free: 10.1 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001444/0.4642, allocations: 0.7746 MB / 0.5664 GB, free: 9.324 MB / 414.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0004055/0.4646, allocations: 136 kB / 0.5665 GB, free: 9.191 MB / 414.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005375/0.47, allocations: 1.697 MB / 0.5682 GB, free: 7.492 MB / 414.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005022/0.4705, allocations: 331 kB / 0.5685 GB, free: 7.168 MB / 414.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0009294/0.4714, allocations: 0.5759 MB / 0.5691 GB, free: 6.59 MB / 414.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.006982/0.4784, allocations: 3.447 MB / 0.5724 GB, free: 3.129 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.326e-06/0.4784, allocations: 0 / 0.5724 GB, free: 3.129 MB / 414.1 MB
Notification: Performance of FrontEnd: time 1.142e-06/0.4784, allocations: 0 / 0.5724 GB, free: 3.129 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 5.288e-05/0.4784, allocations: 0 / 0.5724 GB, free: 3.129 MB / 414.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 276
 * Number of variables: 276
Notification: Performance of Generate backend data structure: time 0.00369/0.4821, allocations: 1.769 MB / 0.5742 GB, free: 1.32 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.213e-05/0.4822, allocations: 12.03 kB / 0.5742 GB, free: 1.309 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001254/0.4834, allocations: 279.5 kB / 0.5745 GB, free: 1.035 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001232/0.4847, allocations: 0.6049 MB / 0.575 GB, free: 416 kB / 414.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001428/0.4848, allocations: 134.1 kB / 0.5752 GB, free: 268 kB / 414.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002125/0.485, allocations: 124.3 kB / 0.5753 GB, free: 144 kB / 414.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002337/0.4873, allocations: 1.333 MB / 0.5766 GB, free: 14.76 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.561e-05/0.4874, allocations: 0 / 0.5766 GB, free: 14.76 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001075/0.4875, allocations: 48 kB / 0.5766 GB, free: 14.71 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.651e-05/0.4875, allocations: 28 kB / 0.5767 GB, free: 14.68 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002832/0.4903, allocations: 1.671 MB / 0.5783 GB, free: 13 MB / 430.1 MB
Warning: The model contains alias variables with redundant start and/or conflicting nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts.
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.006706/0.497, allocations: 3.387 MB / 0.5816 GB, free: 9.531 MB / 430.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003535/0.5006, allocations: 1.871 MB / 0.5834 GB, free: 7.664 MB / 430.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008713/0.5014, allocations: 0.5299 MB / 0.5839 GB, free: 7.129 MB / 430.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006147/0.5076, allocations: 2.794 MB / 0.5867 GB, free: 4.309 MB / 430.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.678e-05/0.5076, allocations: 51.16 kB / 0.5867 GB, free: 4.25 MB / 430.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.054e-06/0.5076, allocations: 0 / 0.5867 GB, free: 4.25 MB / 430.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01436/0.522, allocations: 3.413 MB / 0.5901 GB, free: 0.8008 MB / 430.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.755e-05/0.5221, allocations: 64.41 kB / 0.5901 GB, free: 0.7266 MB / 430.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007302/0.5228, allocations: 0.5701 MB / 0.5907 GB, free: 148 kB / 430.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.506e-05/0.5228, allocations: 41.7 kB / 0.5907 GB, free: 100 kB / 430.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004519/0.5233, allocations: 0.5623 MB / 0.5913 GB, free: 15.53 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003116/0.5236, allocations: 349 kB / 0.5916 GB, free: 15.18 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003641/0.524, allocations: 238.7 kB / 0.5918 GB, free: 14.94 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002048/0.5242, allocations: 386.8 kB / 0.5922 GB, free: 14.55 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006507/0.5248, allocations: 362.5 kB / 0.5925 GB, free: 14.2 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0009886/0.5258, allocations: 0.7477 MB / 0.5933 GB, free: 13.28 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00183/0.5277, allocations: 1.2 MB / 0.5944 GB, free: 11.89 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.213e-05/0.5277, allocations: 4 kB / 0.5944 GB, free: 11.89 MB / 446.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004103/0.5318, allocations: 1.475 MB / 0.5959 GB, free: 10.41 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.788e-05/0.5318, allocations: 14.81 kB / 0.5959 GB, free: 10.39 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.002e-05/0.5318, allocations: 12 kB / 0.5959 GB, free: 10.38 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.00188/0.5337, allocations: 246 kB / 0.5961 GB, free: 10.14 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001423/0.5351, allocations: 327.5 kB / 0.5965 GB, free: 9.816 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005658/0.5408, allocations: 3.587 MB / 0.6 GB, free: 6.027 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0007517/0.5415, allocations: 47.94 kB / 0.6 GB, free: 5.98 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001247/0.5417, allocations: 63.98 kB / 0.6001 GB, free: 5.918 MB / 446.1 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 58
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (152):
 * Single equations (assignments): 150
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of prepare postOptimizeDAE: time 0.0005001/0.5422, allocations: 273.4 kB / 0.6003 GB, free: 5.641 MB / 446.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002333/0.5424, allocations: 79.48 kB / 0.6004 GB, free: 5.562 MB / 446.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004098/0.5465, allocations: 1.335 MB / 0.6017 GB, free: 4.211 MB / 446.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.618e-06/0.5465, allocations: 8 kB / 0.6017 GB, free: 4.203 MB / 446.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.538e-06/0.5465, allocations: 0 / 0.6017 GB, free: 4.203 MB / 446.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.899e-06/0.5465, allocations: 3.984 kB / 0.6017 GB, free: 4.199 MB / 446.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001335/0.5478, allocations: 0.8 MB / 0.6025 GB, free: 3.344 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 8.156e-06/0.5478, allocations: 4 kB / 0.6025 GB, free: 3.34 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001173/0.549, allocations: 215.9 kB / 0.6027 GB, free: 3.129 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001788/0.5508, allocations: 225.6 kB / 0.6029 GB, free: 2.902 MB / 446.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.662e-05/0.5509, allocations: 39.92 kB / 0.603 GB, free: 2.863 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005036/0.5559, allocations: 3.488 MB / 0.6064 GB, free: 15.18 MB / 462.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.027e-06/0.5559, allocations: 4.094 kB / 0.6064 GB, free: 15.17 MB / 462.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004313/0.5602, allocations: 1.733 MB / 0.6081 GB, free: 13.4 MB / 462.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002/0.5604, allocations: 83.38 kB / 0.6081 GB, free: 13.32 MB / 462.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001279/0.5606, allocations: 20 kB / 0.6082 GB, free: 13.3 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005078/0.5611, allocations: 23.94 kB / 0.6082 GB, free: 13.28 MB / 462.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000172/0.5613, allocations: 88.78 kB / 0.6083 GB, free: 13.19 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.08e-05/0.5613, allocations: 39.98 kB / 0.6083 GB, free: 13.15 MB / 462.1 MB
Notification: Performance of sorting global known variables: time 0.0004559/0.5618, allocations: 363.1 kB / 0.6087 GB, free: 12.8 MB / 462.1 MB
Notification: Performance of sort global known variables: time 1.11e-07/0.5618, allocations: 3.938 kB / 0.6087 GB, free: 12.8 MB / 462.1 MB
Notification: Performance of remove unused functions: time 0.00194/0.5637, allocations: 0.674 MB / 0.6093 GB, free: 12.12 MB / 462.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 5
 * Number of states: 5 (solution.temperature,CH4.logn,CO2.logn,H2O.logn,H2.logn)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (98):
 * Single equations (assignments): 96
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.001542/0.5653, allocations: 0.8262 MB / 0.6101 GB, free: 11.29 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.002135/0.5674, allocations: 1.184 MB / 0.6113 GB, free: 10.08 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.905e-06/0.5674, allocations: 3.938 kB / 0.6113 GB, free: 10.07 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001085/0.5685, allocations: 0.7021 MB / 0.612 GB, free: 9.348 MB / 462.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0009156/0.5694, allocations: 193.1 kB / 0.6122 GB, free: 9.16 MB / 462.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003228/0.5726, allocations: 2.005 MB / 0.6141 GB, free: 7.117 MB / 462.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004636/0.5731, allocations: 455.4 kB / 0.6145 GB, free: 6.641 MB / 462.1 MB
Notification: Performance of simCode: alias equations: time 0.0007481/0.5739, allocations: 226.5 kB / 0.6148 GB, free: 6.418 MB / 462.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003259/0.5742, allocations: 154.3 kB / 0.6149 GB, free: 6.27 MB / 462.1 MB
Notification: Performance of SimCode: time 4.61e-07/0.5742, allocations: 4 kB / 0.6149 GB, free: 6.266 MB / 462.1 MB
Notification: Performance of Templates: time 0.03894/0.6131, allocations: 25.34 MB / 0.6397 GB, free: 13.12 MB / 494.1 MB
"
[Timeout remaining time 659]
make -j1 -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 5.816452082246542]
Failed to read output from testmodel.py, exit status != 0:
0.6231723446398973 0.6372449139999999 0.155762525
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f524d386fe0>